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Bibliography Tag: microbiome

Koppel et al., 2017

Koppel, N., Maini Rekdal, V., & Balskus, E. P.; “Chemical transformation of xenobiotics by the human gut microbiota;” Science, 2017, 356(6344); DOI: 10.1126/science.aag2770.


The human gut microbiota makes key contributions to the metabolism of ingested compounds (xenobiotics), transforming hundreds of dietary components, industrial chemicals, and pharmaceuticals into metabolites with altered activities, toxicities, and lifetimes within the body. The chemistry of gut microbial xenobiotic metabolism is often distinct from that of host enzymes. Despite their important consequences for human biology, the gut microbes, genes, and enzymes involved in xenobiotic metabolism are poorly understood. Linking these microbial transformations to enzymes and elucidating their biological effects is undoubtedly challenging. However, recent studies demonstrate that integrating traditional and emerging technologies can enable progress toward this goal. Ultimately, a molecular understanding of gut microbial xenobiotic metabolism will guide personalized medicine and nutrition, inform toxicology risk assessment, and improve drug discovery and development. FULL TEXT

Mesnage, 2019

Mesnage, Robin, “Effects of dietary exposures to pesticide residues on the gut microbiome,” 2019, Presented 10/30/2019 at the London Microbiome Meeting 2019, Great Hall, King’s College London Strand Campus.


The gut microbiota: a major player in the toxicity of environmental pollutants?


Zmora et al., 2019

Zmora, N., Suez, J., & Elinav, E.; “You are what you eat: diet, health and the gut microbiota;” Nature Reviews Gastroenterology and Hepatology, 2019, 16(1), 35-56; DOI: 10.1038/s41575-018-0061-2.


Since the renaissance of microbiome research in the past decade, much insight has accumulated in comprehending forces shaping the architecture and functionality of resident microorganisms in the human gut. Of the multiple host-endogenous and host-exogenous factors involved, diet emerges as a pivotal determinant of gut microbiota community structure and function. By introducing dietary signals into the nexus between the host and its microbiota, nutrition sustains homeostasis or contributes to disease susceptibility. Herein, we summarize major concepts related to the effect of dietary constituents on the gut microbiota, highlighting chief principles in the diet-microbiota crosstalk. We then discuss the health benefits and detrimental consequences that the interactions between dietary and microbial factors elicit in the host. Finally, we present the promises and challenges that arise when seeking to incorporate microbiome data in dietary planning and portray the anticipated revolution that the field of nutrition is facing upon adopting these novel concepts. FULL TEXT

Tsiaoussis et al., 2019

Tsiaoussis, J., Antoniou, M. N., Koliarakis, I., Mesnage, R., Vardavas, C. I., Izotov, B. N., Psaroulaki, A., & Tsatsakis, A.; “Effects of single and combined toxic exposures on the gut microbiome: Current knowledge and future directions;” Toxicology Letters, 2019, 312, 72-97; DOI: 10.1016/j.toxlet.2019.04.014.


Human populations are chronically exposed to mixtures of toxic chemicals. Predicting the health effects of these mixtures require a large amount of information on the mode of action of their components. Xenobiotic metabolism by bacteria inhabiting the gastrointestinal tract has a major influence on human health. Our review aims to explore the literature for studies looking to characterize the different modes of action and outcomes of major chemical pollutants, and some components of cosmetics and food additives, on gut microbial communities in order to facilitate an estimation of their potential mixture effects. We identified good evidence that exposure to heavy metals, pesticides, nanoparticles, polycyclic aromatic hydrocarbons, dioxins, furans, polychlorinated biphenyls, and non-caloric artificial sweeteners affect the gut microbiome and which is associated with the development of metabolic, malignant, inflammatory, or immune diseases. Answering the question ‘Who is there?’ is not sufficient to define the mode of action of a toxicant in predictive modeling of mixture effects. Therefore, we recommend that new studies focus to simulate real-life exposure to diverse chemicals (toxicants, cosmetic/food additives), including as mixtures, and which combine metagenomics, metatranscriptomics and metabolomic analytical methods achieving in that way a comprehensive evaluation of effects on human health. FULL TEXT

Kruger et al., 2013

Kruger, Monika, Shehata, Awad Ali, Schrodl, Wieland, & Rodloff, Arne; “Glyphosate suppresses the antagonistic effect of Enterococcus spp. on Clostridium botulinum;” Anaerobe, 2013, 20, 74-78; DOI: 10.1016/j.anaerobe.2013.01.005.


During the last 10-15 years, an increase of Clostridium botulinum associated diseases in cattle has been observed in Germany. The reason for this development is currently unknown. The normal intestinal microflora is a critical factor in preventing intestinal colonisation by C. botulinum as shown in the mouse model of infant botulism. Numerous bacteria in the gastro-intestinal tract (GIT) produce bacteriocines directed against C. botulinum and other pathogens: Lactic acid producing bacteria (LAB) such as lactobacilli, lactococci and enterococci, generate bacteriocines that are effective against Clostridium spp. A reduction of LAB in the GIT microbiota by ingestion of strong biocides like glyphosate could be an explanation for the observed increase in levels of C. botulinum associated diseases. In the present paper, we report on the toxicity of glyphosate to the most prevalent Enterococcus spp. in the GIT. Ingestion of this herbicide could be a significant predisposing factor that is associated with the increase in C. botulinum mediated diseases in cattle. FULL TEXT

Ackermann et al., 2015

Ackermann, W., Coenen, M., Schrodl, W., Shehata, A. A., & Kruger, M.; “The influence of glyphosate on the microbiota and production of botulinum neurotoxin during ruminal fermentation;” Current Microbiology, 2015, 70(3), 374-382; DOI: 10.1007/s00284-014-0732-3.


The aim of the present study is to investigate the impact of glyphosate on the microbiota and on the botulinum neurotoxin (BoNT) expression during in vitro ruminal fermentation. This study was conducted using two DAISY(II)-incubators with four ventilated incubation vessels filled with rumen fluid of a 4-year-old non-lactating Holstein-Friesian cow. Two hundred milliliter rumen fluid and 800 ml buffer solution were used with six filter bags containing 500 mg concentrated feed or crude fiber-enriched diet. Final concentrations of 0, 1, 10, and 100 microg/ml of glyphosate in the diluted rumen fluids were added and incubated under CO2-aerated conditions for 48 h. The protozoal population was analyzed microscopically and the ruminal flora was characterized using the fluorescence in situ hybridization technique. Clostridium botulinum and BoNT were quantified using most probable number and ELISA, respectively. Results showed that glyphosate had an inhibitory effect on select groups of the ruminal microbiota, but increased the population of pathogenic species. The BoNT was produced during incubation when inoculum was treated with high doses of glyphosate. In conclusion, glyphosate causes dysbiosis which favors the production of BoNT in the rumen. The global regulations restrictions for the use of glyphosate should be re-evaluated. FULL TEXT

Shehata et al., 2013

Shehata, A. A., Schrodl, W., Aldin, A. A., Hafez, H. M., & Kruger, M.; “The effect of glyphosate on potential pathogens and beneficial members of poultry microbiota in vitro;” Current Microbiology, 2013, 66(4), 350-358; DOI: 10.1007/s00284-012-0277-2.


The use of glyphosate modifies the environment which stresses the living microorganisms. The aim of the present study was to determine the real impact of glyphosate on potential pathogens and beneficial members of poultry microbiota in vitro. The presented results evidence that the highly pathogenic bacteria as Salmonella Entritidis, Salmonella Gallinarum, Salmonella Typhimurium, Clostridium perfringens and Clostridium botulinum are highly resistant to glyphosate. However, most of beneficial bacteria as Enterococcus faecalis, Enterococcus faecium, Bacillus badius, Bifidobacterium adolescentis and Lactobacillus spp. were found to be moderate to highly susceptible. Also Campylobacter spp. were found to be susceptible to glyphosate. A reduction of beneficial bacteria in the gastrointestinal tract microbiota by ingestion of glyphosate could disturb the normal gut bacterial community. Also, the toxicity of glyphosate to the most prevalent Enterococcus spp. could be a significant predisposing factor that is associated with the increase in C. botulinum-mediated diseases by suppressing the antagonistic effect of these bacteria on clostridia. FULL TEXT

Tremlett et al, 2017

Tremlett, H., Bauer, K. C., Appel-Cresswell, S., Finlay, B. B., & Waubant, E.; “The gut microbiome in human neurological disease: A review;” Annals of Neurology, 2017, 81(3), 369-382; DOI: 10.1002/ana.24901.


Almost half the cells and 1% of the unique genes found in our bodies are human, the rest are from microbes, predominantly bacteria, archaea, fungi, and viruses. These microorganisms collectively form the human microbiota, with most colonizing the gut. Recent technological advances, open access data libraries, and application of high-throughput sequencing have allowed these microbes to be identified and their contribution to neurological health to be examined. Emerging evidence links perturbations in the gut microbiota to neurological disease, including disease risk, activity, and progression. This review provides an overview of the recent advances in microbiome research in relation to neuro(auto)immune and neurodegenerative conditions affecting humans, such as multiple sclerosis, neuromyelitis optica spectrum disorders, Parkinson disease, Alzheimer disease, Huntington disease, and amyotrophic lateral sclerosis. Study design and terminology used in this rapidly evolving, highly multidisciplinary field are summarized to empower and engage the neurology community in this “newly discovered organ.” FULL TEXT

Mao et al., 2018

Mao, Q., Manservisi, F., Panzacchi, S., Mandrioli, D., Menghetti, I., Vornoli, A., Bua, L., Falcioni, L., Lesseur, C., Chen, J., Belpoggi, F., & Hu, J., “The Ramazzini Institute 13-week pilot study on glyphosate and Roundup administered at human-equivalent dose to Sprague Dawley rats: effects on the microbiome,” Environmental Health, 17(1), 50, 2018. doi:10.1186/s12940-018-0394-x.


BACKGROUND: Glyphosate-based herbicides (GBHs) are broad-spectrum herbicides that act on the shikimate pathway in bacteria, fungi, and plants. The possible effects of GBHs on human health are the subject of an intense public debate for both its potential carcinogenic and non-carcinogenic effects, including its effects on microbiome. The present pilot study examines whether exposure to GBHs at doses of glyphosate considered to be “safe” (the US Acceptable Daily Intake – ADI – of 1.75 mg/kg bw/day), starting from in utero, may modify the composition of gut microbiome in Sprague Dawley (SD) rats.

METHODS: Glyphosate alone and Roundup, a commercial brand of GBHs, were administered in drinking water at doses comparable to the US glyphosate ADI (1.75 mg/kg bw/day) to F0 dams starting from the gestational day (GD) 6 up to postnatal day (PND) 125. Animal feces were collected at multiple time points from both F0 dams and F1 pups. The gut microbiota of 433 fecal samples were profiled at V3-V4 region of 16S ribosomal RNA gene and further taxonomically assigned and assessed for diversity analysis. We tested the effect of exposure on overall microbiome diversity using PERMANOVA and on individual taxa by LEfSe analysis.

RESULTS: Microbiome profiling revealed that low-dose exposure to Roundup and glyphosate resulted in significant and distinctive changes in overall bacterial composition in F1 pups only. Specifically, at PND31, corresponding to pre-pubertal age in humans, relative abundance for Bacteriodetes (Prevotella) was increased while the Firmicutes (Lactobacillus) was reduced in both Roundup and glyphosate exposed F1 pups compared to controls.

CONCLUSIONS: This study provides initial evidence that exposures to commonly used GBHs, at doses considered safe, are capable of modifying the gut microbiota in early development, particularly before the onset of puberty. These findings warrant future studies on potential health effects of GBHs in early development such as childhood. FULL TEXT

van Bruggen et al., 2018

Ariena H.C. van Bruggen, Max Teplitski, Volker Mai, Kwang Cheol Jeong, Joan D. Flocks, Maria R. Finckh, and J. Glenn Morris, Jr., “Environmental and health effects of the herbicide glyphosate,” 2018,  Science of the Total Environment, 2018, 616-617,  DOI: 10.1016/j.scitotenv.2017.10.309.


BACKGROUND: The WHO reclassified the herbicide glyphosate as probably carcinogenic to humans, and concerns about potential side effects of the large-scale use of glyphosate have increased. We are interested in potential indirect effects of glyphosate on animal, human and plant health due to shifts in microbial community composition and antibiotic resistance in soil, plant surfaces and intestinal tracts.

OBJECTIVES: We review the scientific literature on glyphosate use, its toxicity to macro- and microorganisms, effects on microbial compositions, and potential indirect effects on plant, animal and human health. We hypothesize that glyphosate use has increased antibiotic resistance and propose study designs for testing this hypothesis.

DISCUSSION: Although the acute toxic effects of glyphosate on mammals are low, the chronic effects on human and animal health could be considerable due to accumulation in the environment. Intensive glyphosate use has led to the selection of glyphosate-resistant weeds and microorganisms. Shifts in microbial compositions due to selective pressure by glyphosate may have contributed to the proliferation of pathogens. Research on a link between glyphosate and antibiotic resistance is scarce. We hypothesize that the selection pressure for glyphosate resistance in bacteria could lead to shifts in microbiome composition and increases in antibiotic resistance.

CONCLUSION: We recommend interdisciplinary research on the associations between glyphosate use, distortions in microbial communities, expansion of antibiotic resistance and the emergence of animal, human and plant diseases. Independent research is needed to revisit the tolerance thresholds for glyphosate residues in food and animal feed taking all possible health risks into account.  FULL TEXT

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